The Government has rejected Fairfax reports that the Navy fired warning shots at an asylum seeker boat. (File photo)

ADF: Phillip Cullinan

The Government has denied reports the Australian Navy fired warning shots in a bid to force an asylum seeker boat back towards Indonesia.

Fairfax media says an Australian vessel "shot into the air" during the interception of a boat full of asylum seekers within sight of Christmas Island.

The asylum boat was reportedly then forced to return to Indonesia, in what would be the third time the Navy has reportedly forced a boat back in the past month.

But Immigration Minister Scott Morrison says there is no truth to the reports.

"Without commenting on any specific alleged incident I can confirm that no shots have been fired at any time by any persons involved in Operation Sovereign Borders at any time since the operation commenced," he said in a statement.

Opposition Leader Bill Shorten has called on the Government to put an end to the secrecy surrounding its border protection operations.

"I don't want to see servicemen and women caught up as the meat in an Abbott-Morrison secrecy sandwich," he said.

Indonesia considers that many asylum seekers are illegally using the country as a staging point to get to Australia, and objects to them being returned.

Dr Natalegawa has indicated that if Australia is actively helping asylum seekers get back to Indonesia, that is worse.

"It's one thing to turn back the actual boats on which they have been travelling but another issue, when they are transferred onto another boat and facilitated and told to go in that direction," he said.

Dr Natalegawa would not say what action his government would take.

He says with a slow and steady approach, the relationship can be returned to normal and he says the focus on asylum seekers is "unhelpful".

"To be zeroing in on issues that, in a manner that tends to divide, is not helpful," he said.

Yesterday Lieutenant General Angus Campbell, the commander of Operation Sovereign Borders, would not confirm or deny reports the lifeboats would be used to send asylum seekers back to Indonesia.

"We've acquired them to be part of the range of measures that we have at play," he told a media briefing yesterday.

"Clearly a lifeboat, it's involved potentially in those on-water activities that we don't discuss and so I'm not going to go further in that space."

Morrison says confusion over tow backs 'semantics'

Mr Morrison also defended towing boats back towards Indonesia, saying there has never been an intention to enter Indonesian waters.

"Previously, before the election, what had been said and the way tow back as a policy was explained and particularly to the Indonesian government and as it was characterised both in the media and by the previous government is that boats would be towed back into Indonesian waters or towed back to Indonesian ports," he said.

"That was the relevance of the phrase 'tow back'.

"Now, we've said very plainly, and we said this before the election, that it has never been our policy to violate Indonesia's territorial sovereignty.

"So I think there's been confusion on the semantics by some on this and hopefully that clears it up."

Indonesia's minister responsible, Djoko Suyanto, has not responded to the ABC's requests for a comment.

It is understood he has been busy dealing with domestic priorities, like the aftermath of the Mount Sinabung volcano eruption that has left 25,000 Indonesians homeless.

But a senior government source says the issue of turning asylum seeker boats back is unhelpful and Indonesia would rather have another issue to discuss.